Here's the repro steps on the missing key ability modifier...
* Create new character
* Fill in name 'Tester'
* Click ability editor - Stats 10, 12, 12, 15, 10, 11
* Drag 'Human' and drop on race, choose Intelligence to boost
* Drag 'Scholar' and drop on theme - change Key Ability as 'Int' (This is the mistake I made)
* Drag 'Technomancer' and drop on class - notice that it has no key ability - in the XML file under the classes node it is missing classkey and classkeymod